In biological processes the direction an ion will move by diffusion or active transport across membrane is determined by the electrochemical gradient. In mitochondria and chloroplasts, proton gradients are used to generate a chemiosmotic potential that is also known as a proton motive force. This potential energy is used for the synthesis of ATP by oxidative phosphorylation.

An electrochemical gradient has two components. First, the electrical component is caused by a charge difference across the lipid membrane. Second, a chemical component is caused by a differential concentration of ions across the membrane. The combination of these two factors determines the thermodynamically favourable direction for an ions movement across a membrane.

Electrochemical gradients are analogous to hydroelectric dams and equivalent to the water pressure across the dam. Membrane transport proteins such as the sodium-potassium pump within the membrane are equivalent to turbines that convert the waters potential energy to other forms of physical or chemical energy, and the ions that pass through the membrane are equivalent to water that is now found at the bottom of the dam. Alternatively, energy can be used to pump water up into the lake above the dam. Similarly chemical energy in cells can be used to create electrochemical gradients.

In biology, the term is sometimes used in the context of a chemical reaction, in particular to describe the energy source for the chemical synthesis of ATP. More generally, however, it is used to characterize the inclined tendency of solutes to simply diffuse across a membrane, a process involving no chemical transformation.

With respect to a cell, organelle, or other subcellular compartments, the inclined tendency of an electrically charged solute, such as a potassium ion, to move across the membrane is decided by the difference in its electrochemical potential on either side of the membrane, which arises from three factors:

the difference in the concentration of the solute between the two sides of the membrane

A solute's electrochemical potential difference is zero at its "reversal potential". The transmembrane voltage to which the solute's net flow across the membrane is also zero. This potential is predicted theoretically either by the Nernst equation (for systems of one permeant ion species) or the Goldman-Hodgkin-Katz equation (for more than one permeant ion species). Electrochemical potential is measured in the laboratory and field using reference electrodes.

Transmembrane ATPases or transmembrane proteins with ATPase domains are often used for making and utilizing ion gradients. The enzyme Na+/K+ ATPase use ATP to make a sodium ion gradient and a potassium ion gradient. The electrochemical potential is used as energy storage, chemiosmotic coupling is one of several ways a thermodynamically unfavorable reaction can be driven by a thermodynamically favorable one. Cotransport of ions by symporters and antiporter carriers are common to actively move ions across biological membranes.

The proton gradient can be used as an intermediate energy storage for heat production and flagellar rotation. Additionally, it is an interconvertible form of energy in active transport, electron potential generation, NADPH synthesis, and ATP synthesis/hydrolysis.

Proton Motive Force: two protons are expelled at each coupling site, generating the Proton Motive Force. ATP is made indirectly using the PMF as a source of energy. Each pair of protons yields one ATP.

Some archaea, most notably halobacteria, make proton gradients by pumping in protons from the environment with the help of the solar driven enzyme bacteriorhodopsin, here it is used for driving the molecular motor enzyme ATP synthase to make the necessary conformational changes required to synthesize ATP.

Proton gradients are also made by bacteria by running ATP synthase in reverse; this is used to drive flagella.

The F1FO ATP synthase is a reversible enzyme. Large enough quantities of ATP cause it to create a transmembrane protongradient. This is used by fermenting bacteria - which do not have an electron transport chain, and hydrolyze ATP to make a proton gradient - which they use for flagella and the transportation of nutrients into the cell.

In respiring bacteria under physiological conditions, ATP synthase generally runs in the opposite direction creating ATP while using the proton motive force created by the electron transport chain as a source of energy. The overall process of creating energy in this fashion is termed: oxidative phosphorylation. The same process takes place in mitochondria where ATP synthase is located in the inner mitochondrial membrane, so that F1-part sticks into mitochondrial matrix, where ATP synthesis takes place.